Basic overview

Densities of VIM

marker = "VIM"

ggplot(cb_atl) +
        geom_density_ridges(aes(x=get(raw_vars[grepl(marker,raw_vars)]), y = SlideID,fill=SlideID)) +
        ggtitle('Raw data')  +
        theme_minimal() +
        theme(legend.position = "none")
## Picking joint bandwidth of 183

ggplot(cb_atl) +
        geom_density_ridges(aes(x=get(log_vars[grepl(marker,log_vars)]), y = SlideID,fill=SlideID)) +
        ggtitle('Log data')  +
        theme_minimal() +
        theme(legend.position = "none")
## Picking joint bandwidth of 0.102

ggplot(cb_atl) +
        geom_density_ridges(aes(x=get(simple_vars[grepl(marker,simple_vars)]), y = SlideID,fill=SlideID)) +
        ggtitle('Simple adjusted data')  +
        theme_minimal() +
        theme(legend.position = "none") +
        xlim(c(0,5))
## Picking joint bandwidth of 0.117
## Warning: Removed 143274 rows containing non-finite values (stat_density_ridges).

ggplot(cb_atl) +
        geom_density_ridges(aes(x=get(simple_vars_centered[grepl(marker,simple_vars_centered)]), y = SlideID,fill=SlideID)) +
        ggtitle('Simple adjusted data (centered)')  +
        theme_minimal() +
        theme(legend.position = "none") +
        xlim(c(0,5))
## Picking joint bandwidth of 0.0733
## Warning: Removed 765513 rows containing non-finite values (stat_density_ridges).

ggplot(cb_atl) +
        geom_density_ridges(aes(x=get(combat_vars[grepl(marker,combat_vars)]), y = SlideID,fill=SlideID)) +
        ggtitle('ComBat adjusted (slide only)')  +
        theme_minimal() +
        theme(legend.position = "none") +
        xlim(c(0,5))
## Picking joint bandwidth of 0.00231

ggplot(cb_atl) +
        geom_density_ridges(aes(x=get(combat_vars_og[grepl(marker,combat_vars_og)]), y = SlideID,fill=SlideID)) +
        ggtitle('ComBat adjusted (original method)')  +
        theme_minimal() +
        theme(legend.position = "none")
## Picking joint bandwidth of 0.0357

ggplot(cb_atl) +
        geom_density_ridges(aes(x=get(combat_vars_p[grepl(marker,combat_vars_p)]), y = SlideID,fill=SlideID)) +
        ggtitle('ComBat adjusted (slide only, with image level variance)')  +
        theme_minimal() +
        theme(legend.position = "none")
## Picking joint bandwidth of 0.0401

ggplot(cb_atl) +
        geom_density_ridges(aes(x=get(simple2_vars[grepl(marker,simple2_vars)]), y = SlideID,fill=SlideID)) +
        ggtitle('Simple2 adjustment')  +
        theme_minimal() +
        theme(legend.position = "none") +
        xlim(c(0,10))
## Picking joint bandwidth of 0.178
## Warning: Removed 52214 rows containing non-finite values (stat_density_ridges).

ggplot(cb_atl) +
        geom_density_ridges(aes(x=get(modal_vars[grepl(marker,modal_vars)]), y = SlideID,fill=SlideID)) +
        ggtitle('Simple modal adjustment')  +
        theme_minimal() +
        theme(legend.position = "none")
## Picking joint bandwidth of 0.102

ggplot(cb_atl) +
        geom_density_ridges(aes(x=get(modal_vars_zeroes_removed[grepl(marker,modal_vars_zeroes_removed)]), y = SlideID,fill=SlideID)) +
        ggtitle('Simple modal adjustment (zeroes removed)')  +
        theme_minimal() +
        theme(legend.position = "none")
## Picking joint bandwidth of 0.103

registr

## registr
registr_data = data.frame()
for(s in unique(cb_atl$SlideID)){
  dv = density(cb_atl[cb_atl$SlideID == s,
                      'Median_Cell_VIMENTIN_log10'])
  one_slide = data.frame(dv$x,dv$y)
  one_slide$slide = s
  registr_data = rbind(registr_data,one_slide)
}
colnames(registr_data) = c("index","value","id")


## Kt=7, Kh=3: 589
## Kt=8, Kh=5: 560
## Kt=9, Kh=4: 539
## Kt=10, Kh=5: 519
## Kt=11, Kh=4: 314
## Kt=12, Kh=5: 305

registr_bin1 = register_fpca(Y = registr_data,
                            family = "gaussian")
registr_bin2 = register_fpca(Y = registr_data,
                            family = "gaussian",
                            Kt = 9,
                            Kh = 4,
                            npc = 1)
registr_bin3 = register_fpca(Y = registr_data,
                            family = "gaussian",
                            Kt = 12,
                            Kh = 5,
                            npc = 1)

## remove the zeroes

## log10 data
ggplot(registr_data) +
  geom_line(aes(x=index,y=value,color=id)) +
  theme(legend.position = "None")

## Modal adjustment
ggplot(cb_atl) + 
  geom_density(aes(x=Median_Cell_VIMENTIN_log10_modal_adjusted_zeroes_removed,color=SlideID)) +
  theme(legend.position = "None")

registr_adj_data1 = registr_bin1$fpca_obj$Yhat
ggplot(registr_adj_data1) +
  geom_line(aes(x=index,y=value,color=id)) +
  theme(legend.position = "None")

registr_adj_data2 = registr_bin2$fpca_obj$Yhat
ggplot(registr_adj_data2) +
  geom_line(aes(x=index,y=value,color=id)) +
  theme(legend.position = "None")

registr_adj_data3 = registr_bin3$fpca_obj$Yhat
ggplot(registr_adj_data3) +
  geom_line(aes(x=index,y=value,color=id)) +
  theme(legend.position = "None")

In log-transformed space

for(c in all_clus){
 gc1 = ggpairs(plot_atl_raw,
        columns=4:6,
        lower=list(continuous = wrap("points",alpha=0.25)),
        ggplot2::aes(color=get(c)),
        title = paste0(c," in log-transformed space")) +
        theme_minimal()
 print(gc1)
}

Confusion matrices

for(c in all_clus[-3]){
        ## truth: within slide, prediction: across slide
        cmat1 = confusionMatrix(data = as.data.frame(cb_atl)[,c],
                                reference = cb_atl$cluster_within_slide_log)
        
        print("---------------------------------")
        print("---------------------------------")
        print("---------------------------------")
        print(paste0(c," compared to cluster_within_slide_log"))
        print(cmat1)
}
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "cluster_within_slide_raw compared to cluster_within_slide_log"
## Confusion Matrix and Statistics
## 
##           Reference
## Prediction       1       2
##          1 1189901  250853
##          2  648599 1504119
##                                           
##                Accuracy : 0.7497          
##                  95% CI : (0.7493, 0.7501)
##     No Information Rate : 0.5116          
##     P-Value [Acc > NIR] : < 2.2e-16       
##                                           
##                   Kappa : 0.5017          
##                                           
##  Mcnemar's Test P-Value : < 2.2e-16       
##                                           
##             Sensitivity : 0.6472          
##             Specificity : 0.8571          
##          Pos Pred Value : 0.8259          
##          Neg Pred Value : 0.6987          
##              Prevalence : 0.5116          
##          Detection Rate : 0.3311          
##    Detection Prevalence : 0.4009          
##       Balanced Accuracy : 0.7521          
##                                           
##        'Positive' Class : 1               
##                                           
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "cluster_across_slide_raw compared to cluster_within_slide_log"
## Confusion Matrix and Statistics
## 
##           Reference
## Prediction       1       2
##          1 1440691 1725791
##          2  397809   29181
##                                           
##                Accuracy : 0.409           
##                  95% CI : (0.4085, 0.4095)
##     No Information Rate : 0.5116          
##     P-Value [Acc > NIR] : 1               
##                                           
##                   Kappa : -0.2032         
##                                           
##  Mcnemar's Test P-Value : <2e-16          
##                                           
##             Sensitivity : 0.78362         
##             Specificity : 0.01663         
##          Pos Pred Value : 0.45498         
##          Neg Pred Value : 0.06834         
##              Prevalence : 0.51162         
##          Detection Rate : 0.40092         
##    Detection Prevalence : 0.88118         
##       Balanced Accuracy : 0.40013         
##                                           
##        'Positive' Class : 1               
##                                           
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "cluster_across_slide_log compared to cluster_within_slide_log"
## Confusion Matrix and Statistics
## 
##           Reference
## Prediction       1       2
##          1 1572782  148389
##          2  265718 1606583
##                                           
##                Accuracy : 0.8848          
##                  95% CI : (0.8844, 0.8851)
##     No Information Rate : 0.5116          
##     P-Value [Acc > NIR] : < 2.2e-16       
##                                           
##                   Kappa : 0.7697          
##                                           
##  Mcnemar's Test P-Value : < 2.2e-16       
##                                           
##             Sensitivity : 0.8555          
##             Specificity : 0.9154          
##          Pos Pred Value : 0.9138          
##          Neg Pred Value : 0.8581          
##              Prevalence : 0.5116          
##          Detection Rate : 0.4377          
##    Detection Prevalence : 0.4790          
##       Balanced Accuracy : 0.8855          
##                                           
##        'Positive' Class : 1               
##                                           
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "cluster_within_slide_simple compared to cluster_within_slide_log"
## Confusion Matrix and Statistics
## 
##           Reference
## Prediction       1       2
##          1 1435282  104461
##          2  403218 1650511
##                                           
##                Accuracy : 0.8587          
##                  95% CI : (0.8584, 0.8591)
##     No Information Rate : 0.5116          
##     P-Value [Acc > NIR] : < 2.2e-16       
##                                           
##                   Kappa : 0.7184          
##                                           
##  Mcnemar's Test P-Value : < 2.2e-16       
##                                           
##             Sensitivity : 0.7807          
##             Specificity : 0.9405          
##          Pos Pred Value : 0.9322          
##          Neg Pred Value : 0.8037          
##              Prevalence : 0.5116          
##          Detection Rate : 0.3994          
##    Detection Prevalence : 0.4285          
##       Balanced Accuracy : 0.8606          
##                                           
##        'Positive' Class : 1               
##                                           
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "cluster_across_slide_simple compared to cluster_within_slide_log"
## Confusion Matrix and Statistics
## 
##           Reference
## Prediction       1       2
##          1 1232268  113544
##          2  606232 1641428
##                                           
##                Accuracy : 0.7997          
##                  95% CI : (0.7993, 0.8001)
##     No Information Rate : 0.5116          
##     P-Value [Acc > NIR] : < 2.2e-16       
##                                           
##                   Kappa : 0.6017          
##                                           
##  Mcnemar's Test P-Value : < 2.2e-16       
##                                           
##             Sensitivity : 0.6703          
##             Specificity : 0.9353          
##          Pos Pred Value : 0.9156          
##          Neg Pred Value : 0.7303          
##              Prevalence : 0.5116          
##          Detection Rate : 0.3429          
##    Detection Prevalence : 0.3745          
##       Balanced Accuracy : 0.8028          
##                                           
##        'Positive' Class : 1               
##                                           
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "cluster_within_slide_cb compared to cluster_within_slide_log"
## Confusion Matrix and Statistics
## 
##           Reference
## Prediction       1       2
##          1 1790548   15859
##          2   47952 1739113
##                                           
##                Accuracy : 0.9822          
##                  95% CI : (0.9821, 0.9824)
##     No Information Rate : 0.5116          
##     P-Value [Acc > NIR] : < 2.2e-16       
##                                           
##                   Kappa : 0.9645          
##                                           
##  Mcnemar's Test P-Value : < 2.2e-16       
##                                           
##             Sensitivity : 0.9739          
##             Specificity : 0.9910          
##          Pos Pred Value : 0.9912          
##          Neg Pred Value : 0.9732          
##              Prevalence : 0.5116          
##          Detection Rate : 0.4983          
##    Detection Prevalence : 0.5027          
##       Balanced Accuracy : 0.9824          
##                                           
##        'Positive' Class : 1               
##                                           
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "cluster_across_slide_cb compared to cluster_within_slide_log"
## Confusion Matrix and Statistics
## 
##           Reference
## Prediction       1       2
##          1 1092613 1750934
##          2  745887    4038
##                                           
##                Accuracy : 0.3052          
##                  95% CI : (0.3047, 0.3057)
##     No Information Rate : 0.5116          
##     P-Value [Acc > NIR] : 1               
##                                           
##                   Kappa : -0.4087         
##                                           
##  Mcnemar's Test P-Value : <2e-16          
##                                           
##             Sensitivity : 0.594296        
##             Specificity : 0.002301        
##          Pos Pred Value : 0.384243        
##          Neg Pred Value : 0.005385        
##              Prevalence : 0.511622        
##          Detection Rate : 0.304055        
##    Detection Prevalence : 0.791309        
##       Balanced Accuracy : 0.298298        
##                                           
##        'Positive' Class : 1               
##                                           
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "cluster_within_slide_simple_centered compared to cluster_within_slide_log"
## Confusion Matrix and Statistics
## 
##           Reference
## Prediction       1       2
##          1 1597073   34729
##          2  241427 1720243
##                                           
##                Accuracy : 0.9232          
##                  95% CI : (0.9229, 0.9234)
##     No Information Rate : 0.5116          
##     P-Value [Acc > NIR] : < 2.2e-16       
##                                           
##                   Kappa : 0.8466          
##                                           
##  Mcnemar's Test P-Value : < 2.2e-16       
##                                           
##             Sensitivity : 0.8687          
##             Specificity : 0.9802          
##          Pos Pred Value : 0.9787          
##          Neg Pred Value : 0.8769          
##              Prevalence : 0.5116          
##          Detection Rate : 0.4444          
##    Detection Prevalence : 0.4541          
##       Balanced Accuracy : 0.9244          
##                                           
##        'Positive' Class : 1               
##                                           
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "cluster_across_slide_simple_centered compared to cluster_within_slide_log"
## Confusion Matrix and Statistics
## 
##           Reference
## Prediction       1       2
##          1 1229879  113473
##          2  608621 1641499
##                                           
##                Accuracy : 0.7991          
##                  95% CI : (0.7986, 0.7995)
##     No Information Rate : 0.5116          
##     P-Value [Acc > NIR] : < 2.2e-16       
##                                           
##                   Kappa : 0.6005          
##                                           
##  Mcnemar's Test P-Value : < 2.2e-16       
##                                           
##             Sensitivity : 0.6690          
##             Specificity : 0.9353          
##          Pos Pred Value : 0.9155          
##          Neg Pred Value : 0.7295          
##              Prevalence : 0.5116          
##          Detection Rate : 0.3423          
##    Detection Prevalence : 0.3738          
##       Balanced Accuracy : 0.8021          
##                                           
##        'Positive' Class : 1               
##                                           
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "cluster_within_slide_og_combat compared to cluster_within_slide_log"
## Confusion Matrix and Statistics
## 
##           Reference
## Prediction       1       2
##          1 1673617  168303
##          2  164883 1586669
##                                          
##                Accuracy : 0.9073         
##                  95% CI : (0.907, 0.9076)
##     No Information Rate : 0.5116         
##     P-Value [Acc > NIR] : < 2.2e-16      
##                                          
##                   Kappa : 0.8145         
##                                          
##  Mcnemar's Test P-Value : 3.158e-09      
##                                          
##             Sensitivity : 0.9103         
##             Specificity : 0.9041         
##          Pos Pred Value : 0.9086         
##          Neg Pred Value : 0.9059         
##              Prevalence : 0.5116         
##          Detection Rate : 0.4657         
##    Detection Prevalence : 0.5126         
##       Balanced Accuracy : 0.9072         
##                                          
##        'Positive' Class : 1              
##                                          
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "cluster_across_slide_og_combat compared to cluster_within_slide_log"
## Confusion Matrix and Statistics
## 
##           Reference
## Prediction       1       2
##          1 1788326 1562802
##          2   50174  192170
##                                           
##                Accuracy : 0.5511          
##                  95% CI : (0.5506, 0.5517)
##     No Information Rate : 0.5116          
##     P-Value [Acc > NIR] : < 2.2e-16       
##                                           
##                   Kappa : 0.0839          
##                                           
##  Mcnemar's Test P-Value : < 2.2e-16       
##                                           
##             Sensitivity : 0.9727          
##             Specificity : 0.1095          
##          Pos Pred Value : 0.5336          
##          Neg Pred Value : 0.7930          
##              Prevalence : 0.5116          
##          Detection Rate : 0.4977          
##    Detection Prevalence : 0.9326          
##       Balanced Accuracy : 0.5411          
##                                           
##        'Positive' Class : 1               
##                                           
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "cluster_within_slide_cb_slide_with_image_variance compared to cluster_within_slide_log"
## Confusion Matrix and Statistics
## 
##           Reference
## Prediction       1       2
##          1 1509069  186306
##          2  329431 1568666
##                                           
##                Accuracy : 0.8565          
##                  95% CI : (0.8561, 0.8568)
##     No Information Rate : 0.5116          
##     P-Value [Acc > NIR] : < 2.2e-16       
##                                           
##                   Kappa : 0.7133          
##                                           
##  Mcnemar's Test P-Value : < 2.2e-16       
##                                           
##             Sensitivity : 0.8208          
##             Specificity : 0.8938          
##          Pos Pred Value : 0.8901          
##          Neg Pred Value : 0.8264          
##              Prevalence : 0.5116          
##          Detection Rate : 0.4199          
##    Detection Prevalence : 0.4718          
##       Balanced Accuracy : 0.8573          
##                                           
##        'Positive' Class : 1               
##                                           
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "cluster_across_slide_cb_slide_with_image_variance compared to cluster_within_slide_log"
## Confusion Matrix and Statistics
## 
##           Reference
## Prediction       1       2
##          1 1694517 1741977
##          2  143983   12995
##                                           
##                Accuracy : 0.4752          
##                  95% CI : (0.4747, 0.4757)
##     No Information Rate : 0.5116          
##     P-Value [Acc > NIR] : 1               
##                                           
##                   Kappa : -0.0724         
##                                           
##  Mcnemar's Test P-Value : <2e-16          
##                                           
##             Sensitivity : 0.921685        
##             Specificity : 0.007405        
##          Pos Pred Value : 0.493095        
##          Neg Pred Value : 0.082782        
##              Prevalence : 0.511622        
##          Detection Rate : 0.471554        
##    Detection Prevalence : 0.956316        
##       Balanced Accuracy : 0.464545        
##                                           
##        'Positive' Class : 1               
##                                           
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "cluster_within_slide_simple2 compared to cluster_within_slide_log"
## Confusion Matrix and Statistics
## 
##           Reference
## Prediction       1       2
##          1 1535152  112409
##          2  303348 1642563
##                                          
##                Accuracy : 0.8843         
##                  95% CI : (0.884, 0.8846)
##     No Information Rate : 0.5116         
##     P-Value [Acc > NIR] : < 2.2e-16      
##                                          
##                   Kappa : 0.769          
##                                          
##  Mcnemar's Test P-Value : < 2.2e-16      
##                                          
##             Sensitivity : 0.8350         
##             Specificity : 0.9359         
##          Pos Pred Value : 0.9318         
##          Neg Pred Value : 0.8441         
##              Prevalence : 0.5116         
##          Detection Rate : 0.4272         
##    Detection Prevalence : 0.4585         
##       Balanced Accuracy : 0.8855         
##                                          
##        'Positive' Class : 1              
##                                          
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "cluster_across_slide_simple2 compared to cluster_within_slide_log"
## Confusion Matrix and Statistics
## 
##           Reference
## Prediction       1       2
##          1 1459036  121517
##          2  379464 1633455
##                                           
##                Accuracy : 0.8606          
##                  95% CI : (0.8602, 0.8609)
##     No Information Rate : 0.5116          
##     P-Value [Acc > NIR] : < 2.2e-16       
##                                           
##                   Kappa : 0.7219          
##                                           
##  Mcnemar's Test P-Value : < 2.2e-16       
##                                           
##             Sensitivity : 0.7936          
##             Specificity : 0.9308          
##          Pos Pred Value : 0.9231          
##          Neg Pred Value : 0.8115          
##              Prevalence : 0.5116          
##          Detection Rate : 0.4060          
##    Detection Prevalence : 0.4398          
##       Balanced Accuracy : 0.8622          
##                                           
##        'Positive' Class : 1               
##                                           
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "cluster_within_slide_simple_modal compared to cluster_within_slide_log"
## Confusion Matrix and Statistics
## 
##           Reference
## Prediction       1       2
##          1 1628559  106002
##          2  209941 1648970
##                                           
##                Accuracy : 0.9121          
##                  95% CI : (0.9118, 0.9124)
##     No Information Rate : 0.5116          
##     P-Value [Acc > NIR] : < 2.2e-16       
##                                           
##                   Kappa : 0.8243          
##                                           
##  Mcnemar's Test P-Value : < 2.2e-16       
##                                           
##             Sensitivity : 0.8858          
##             Specificity : 0.9396          
##          Pos Pred Value : 0.9389          
##          Neg Pred Value : 0.8871          
##              Prevalence : 0.5116          
##          Detection Rate : 0.4532          
##    Detection Prevalence : 0.4827          
##       Balanced Accuracy : 0.9127          
##                                           
##        'Positive' Class : 1               
##                                           
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "cluster_across_slide_simple_modal compared to cluster_within_slide_log"
## Confusion Matrix and Statistics
## 
##           Reference
## Prediction       1       2
##          1 1579717  154531
##          2  258783 1600441
##                                           
##                Accuracy : 0.885           
##                  95% CI : (0.8847, 0.8853)
##     No Information Rate : 0.5116          
##     P-Value [Acc > NIR] : < 2.2e-16       
##                                           
##                   Kappa : 0.7701          
##                                           
##  Mcnemar's Test P-Value : < 2.2e-16       
##                                           
##             Sensitivity : 0.8592          
##             Specificity : 0.9119          
##          Pos Pred Value : 0.9109          
##          Neg Pred Value : 0.8608          
##              Prevalence : 0.5116          
##          Detection Rate : 0.4396          
##    Detection Prevalence : 0.4826          
##       Balanced Accuracy : 0.8856          
##                                           
##        'Positive' Class : 1               
##                                           
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "cluster_within_slide_modal_adjusted_zeroes_removed compared to cluster_within_slide_log"
## Confusion Matrix and Statistics
## 
##           Reference
## Prediction       1       2
##          1 1835939    4278
##          2    2561 1750694
##                                           
##                Accuracy : 0.9981          
##                  95% CI : (0.9981, 0.9981)
##     No Information Rate : 0.5116          
##     P-Value [Acc > NIR] : < 2.2e-16       
##                                           
##                   Kappa : 0.9962          
##                                           
##  Mcnemar's Test P-Value : < 2.2e-16       
##                                           
##             Sensitivity : 0.9986          
##             Specificity : 0.9976          
##          Pos Pred Value : 0.9977          
##          Neg Pred Value : 0.9985          
##              Prevalence : 0.5116          
##          Detection Rate : 0.5109          
##    Detection Prevalence : 0.5121          
##       Balanced Accuracy : 0.9981          
##                                           
##        'Positive' Class : 1               
##                                           
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "---------------------------------"
## [1] "cluster_across_slide_modal_adjusted_zeroes_removed compared to cluster_within_slide_log"
## Confusion Matrix and Statistics
## 
##           Reference
## Prediction       1       2
##          1 1581075  158088
##          2  257425 1596884
##                                          
##                Accuracy : 0.8844         
##                  95% CI : (0.884, 0.8847)
##     No Information Rate : 0.5116         
##     P-Value [Acc > NIR] : < 2.2e-16      
##                                          
##                   Kappa : 0.7689         
##                                          
##  Mcnemar's Test P-Value : < 2.2e-16      
##                                          
##             Sensitivity : 0.8600         
##             Specificity : 0.9099         
##          Pos Pred Value : 0.9091         
##          Neg Pred Value : 0.8612         
##              Prevalence : 0.5116         
##          Detection Rate : 0.4400         
##    Detection Prevalence : 0.4840         
##       Balanced Accuracy : 0.8850         
##                                          
##        'Positive' Class : 1              
## 

What now?